EngineeringAdvances

at theUniversity ofNotre Dame

Volume 6, Number 1Summer 2004

nano and biosensors

molecularbiology

n previous issues of this magazine, we’ve indicatedthat a key guiding principle for charting newdirections in research is one of thinking strategicallyand acting collaboratively. That is, we endeavor to focus on important areas of technology and, in each area, to establish a critical mass of intellec-tual and physical resources that enable us to have

a significant impact on the field. This approach hasserved us well in areas such as nanotechnology, wire-less communications, high-performance computing,and the mitigation of natural hazards. In all but onecase, we were fortunate to have been able to launchour efforts from an existing base of excellent faculty.The one exception is in bioengineering.

The term bioengineering encompasses manyactivities, ranging from the development of medicaldevices and processes to the remediation of organicwastes. Five years ago, we recognized the need toestablish a presence in the field, but to do so, wewould have to begin from a virtually nonexistentbase. One of the issues that had to be addressed waswhether to move in the direction of establishing aseparate department, or to integrate activities within

existing departments. For two reasons, we adopted the second approach.

One reason was related to the reality of limitedresources and the fact that establishment of a newdepartment would adversely affect existing depart-ments. The second reason related to our belief that a bioengineer is first and foremost an engineer.Accordingly, it was felt that our students would bebetter served by becoming well grounded in one ofthe traditional engineering disciplines and by appro-priately integrating biological/medical issues. Formany years this premise has been affirmed by corpo-rations rooted in biomedical technologies throughtheir preference for recruiting graduates with strongbackgrounds in fields such as chemical, electrical, ormechanical engineering, with the understanding thatthey, the corporations, would provide the requisite bio-medical background. The same inputs are receivedtoday from a range of corporate sectors, such as medical electronics, orthopedics, and pharmaceuticals.

Thus far our strategy has worked well. Withinthree of our departments (Aerospace and MechanicalEngineering, Chemical and Biomolecular Engineering,and Civil Engineering and Geological Sciences), bio-engineering has emerged as a major thrust. Significantactivities are also under way in our other departments,Electrical and Computer Science and Engineering.Collectively, research encompasses a broad range of topics such as orthopedic implants, biomaterials,reconstruction of medical images, and developmentof a host of diagnostic tools linked to micro fabrica-tion technologies. Many of these activities weredescribed in a previous issue of this magazine (Vol. 4,No. 1, pp. 18-39, 2002), and in this issue we arepleased to report on more recent endeavors relating to research at the intersection of bio and nano tech-nologies, devices for the rapid detection of biotoxins,improvements in radiation therapy, and establishmentof a new Center for Microfluidics and MedicalDiagnostics. Consistent with our commitment to excellence in both education and research, all of theseactivities involve extensive participation of undergrad-uate and, in some cases, high school students.

In this issue of Signatures, we also describe a majorchange to our first-year chemistry sequence, one thatrecognizes the importance of advances in molecularand cellular biology to technologies of the 21st century. Effective this past academic year, all of ourfirst-year engineering intents must take a second-semester chemistry course that is strongly linked tomolecular biology. We believe this change will betterprepare our students for the future, and we are onlythe second college of engineering in the United Statesto have implemented such a requirement.

We hope you find the contents of this issueinformative, and as always, we welcome your comments.

Frank P. IncroperaMatthew H. McCloskey Dean of EngineeringH. Clifford and Evelyn A. Brosey Professor of Mechanical Engineering

I

the dean’sview

Editor

Nina Welding

Production

Joanne Birdsell

Marty Schalm

Photography

Matt Cashore

S I G N A T U R E S is published biannually

by the College of Engineering at the University

of Notre Dame. Subscriptions are free;

requests should be submitted to the address

indicated below. Material may not be

reproduced without permission. For further

information, contact:

Dr. Frank P. Incropera

Matthew H. McCloskey Dean of Engineering

257 Fitzpatrick Hall

Notre Dame, IN 46556-5637

Phone: (574) 631-5530

Fax: (574) 631-8007

URL: http://www.nd.edu/~engineer

Evidence ofThings Not Seen

Nanobiotechnology at theUniversity of Notre Dame

It’s a SmallWorldIntegrating Biology into theEngineering Curriculum

20 College News

24 Department News

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The worthiness of a field of study

or the benefit of combining technologies

— such as the integration of nanoscience and biotechnology —

becomes most apparent when engineers explore

how it can be applied across many disciplines

to improve the quality of life.

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In the first volume of his journal The Writings of

Henry David Thoreau, in the letter describing “A

Week on the Concord and Merrimack Rivers,”

the philosopher, author, and naturalist said,

“The newest is but the oldest made visible to

our senses.” His reflection is as true now as it

was in 1849. People perceive truth from what

they see, and from what they cannot see they

extrapolate, reason, trust, or fabricate. When

they are finally able to visualize an item or

idea, it is not necessarily “new.” More than

likely it was there all along. Perhaps this is

why researchers continually look for ways to

see beyond the immediately visible. They

explore, observe, and record the “invisible,”

so that they can better understand what they

are able to see and then begin to use that

knowledge.

Such is the case with the nano- and biosen-

sor research being conducted at the University

of Notre Dame, as some of the “invisibles” that

faculty in the College of Engineering have been

exploring involve activities on the nano scale.

Nanotechnology describes the process of creat-

ing new structures or systems atom by atom. It

focuses on materials whose components exhib-

it novel properties — physical, chemical, and

biological — due to their size: from a single

nanometer to 100 nanometers. And, its

potential is enormous. According to

the June 2004 issue of Physics

Today, “Scientists predict

that applications of nan-

otechnology will go far

beyond their current uses

— in sunblock, stain-

resistant clothing, and

catalysts — to, for example,

environmental

remediation, power transmis-

sion, and disease diagnosis and

treatment.” Because researchers and

investors continue to envision a world

with molecule-sized clot-breaking machines

and drug-delivery devices, the annual world-

wide investment in nanotechnology has

exceeded $3.5 billion.

Another “invisible” that’s gained impetus

in the last few years is biotechnology, which

uses living organisms and their by-products

to develop or improve plants, animals, and

products for specific purposes.

Early “biotechnology”

included plant and

animal breeding

techniques and the use

of yeast in making beer,

bread, and wine. Today,

biotechnology includes

manipulating genes to

tailor new types of living

cells for emerging environmental

and industrial needs.

Researchers suggest that the potential of the

interface of these two key technologies, which

has proven to be truly multidisciplinary, lies in

the fact that nanotechnology operates at the

same level — the molecular or subcellular scale

— as biological processes. This new field,

which some call nanobiotechnology, integrates

elements of nanotechnology and biotechnolo-

gy in order to develop solutions for some of

the problems facing society today, including

challenges in the medical, information technol-

ogy, security, and aerospace industries, as well

as in environmental protection.

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One of the hottest topics in nanobiotechnology

is its potential for medical applications,

especially in the areas of drug delivery and

diagnostic devices. Agnes E. Ostafin, assistant

professor of chemical and biomolecular engi-

neering, believes that living cells themselves

may provide the best clues for developing

materials suitable for use as biosensors or

drug-delivery vehicles. “One of the projects

we’ve been working on,” she says, “involves

red blood cells.” These cells are attractive for

research because they have a specific function:

They transport oxygen through capillaries to

cells. To do this, they have to be flexible

enough to change shape, fitting within different

sized capillaries as they travel through the body.

According to Ostafin, the red blood cells of

diabetics or people with sickle cell anemia are

unusually rigid. They can’t bend or change

their shape easily, which can lead to blood

clots or strokes. “In our studies,” she says,

“we’ve been paying special attention to the

proteins within cells. What gives some cells

their shape — red blood cells in this

case — is a meshwork of proteins.”

Ostafin explains that this mesh-

work responds differently to

different biochemical sig-

nals. Under certain

circumstances,

the mesh

opens,

In the Nanoscale Bioengineering Laboratory first-year engineeringundergraduate John Maddox classifies and calculates the kineticsof shell formation. He is also attempting to determine the encap-sulation efficiency of a variety of dyes and to identify ways of controlling the final shell thickness. Maddox is assisting Agnes E. Ostafin, assistant professor of chemical and biomolecular engineering, and graduate student Tyler Schmidt.

allowing interaction with the triggering chemi-

cal. At other times, the mesh remains closed.

“Once we understand the situations which

make this mesh open and close,” says Ostafin,

“we can begin to apply that knowledge to

create synthetic meshes. Or perhaps we could

deliver a drug that would help a cell regulate

its sensing of chemicals, so it would begin to

function more normally. We could develop syn-

thetic cells (or bags) that could carry a drug to

a selected site in the body and then, using the

concept of opening and closing the meshwork,

design it to interact with the chemical condi-

tions of a specific disease. These are all possibil-

ities, but first we must understand the physical

biochemical reactions that are taking place.”

Another project directed by Ostafin involves

the self-assembly of nanoshells. These shells,

whose hollow cores are approximately 100

nanometers in diameter (the size of one

human gene), are so small that they do not

behave as expected: Semiconductor materials a

few nanometers large begin to emit light, met-

als become catalytic, and interfacial chemistry

dominates kinetics and particle dynamics. “Our

goal is to find out how we can learn to control

molecular assembly,” says Ostafin, “to make a

molecule brighter or to control a chemical reac-

tion, possibly preserving it within a solvent-

filled core — so it occurs more efficiently.”

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Ostafin and her team have many questions

to answer, but the first step, she contends,

always involves basic studies. Working with

several graduate and undergraduate students,

Ostafin has shown that dye molecules placed

inside nanoshells glow brightly. “We’ve been

working on this project for some time and have

developed many different recipes to make a

variety of particles,” she says. “We believe they

could prove to be useful mobile sensors,

perhaps even tracking cancer in the body.”

According to Ostafin, coating the outer

surface of the nanoshells with other chemicals

helps the structures evade the body’s immune

system while targeting specific tissues. “Once

the shells have attached to the target,” she says,

“they ‘glow,’ making the targeted molecule or

cell much easier to see for diagnostic purposes.

At that point we can consider tailoring the dis-

assembly of the nanoshells, so that they can

either deliver a therapeutic payload to the site

or signal physicians when the biochemical

environment near the targeted tissue is abnor-

mal. This additional information would

improve a physician’s ability to design a treat-

ment regime or track a patient’s progress.”

As part of a project aimed at creating an early cancerdetection nanoprobe, Susan Fath, a rising junior in theDepartment of Chemical and Biomolecular Engineering,studies the kinetics of the chemiluminescent reactionbetween luminol and peroxide. She is working with AgnesE. Ostafin, assistant professor of chemical and biomolecu-lar engineering, and graduate student Philip A. Wingert.

For more information on Ostafin’s research, visit www.nd.edu/~aostafin.

Ostafin stresses that her team

is not developing “a cure for cancer,”

although she is excited about the poten-

tial medical applications of this research.

“The most important thing to remember about

the nano- and bioengineering efforts at Notre

Dame is that there’s scientific merit in the work

that’s occurring throughout the college,” she

says. “When we understand a system, and why

and how it works, that’s when we’ve really

opened the door for discovery and

innovation.”

In fact, a basic understanding of biotechnol-

ogy is the focus of a laboratory course elective

for seniors that Ostafin will be introducing this

fall within the Department of Chemical and

Biomolecular Engineering. Ostafin believes the

lab experience will give students hands-on

opportunities to use the tools of biotechnology,

allowing them to contribute more meaningful-

ly to this growing field.

Nanoscience research was not new to the College of

Engineering when the Center for Nano Science and

Technology was established in 1999. In fact, the creation

of the center culminated 15 years of faculty research

and development in this area. Led by the Department

of Electrical Engineering since its inception, the center

continues to explore the fundamental concepts of

nanoscience in order to develop unique engineering

applications. It integrates research in biological,

molecular, and semiconductor-based nano-structures;

device concepts and modeling; nanofabrication and

characterization; and information processing architectures

and design.

Activities in the center include multidisciplinary

projects in Quantum-dot Cellular Automata, a paradigm

for transistorless computing pioneered at the University;

resonant-tunneling devices and circuits; photonic

integrated circuits; quantum transport and hot carrier

effects in nanodevices; optical and high-speed nano-based

materials, devices, and circuits; the role of non-equilibrium

thermodynamics in influencing the properties of

nanodevices; and the interaction of biological systems

with semiconductors.

“One of the current projects,” says Wolfgang Porod,

center director and Freimann Professor of Electrical

Engineering, “focuses on developing a new generation of

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parallel processing chips that can capture both visible and

invisible — infrared — light. It’s very exciting because

we’re using the mammalian retina, specifically the way the

sensors in an eye are connected, as a model for the vision

sensors which will be placed on these chips.”

The project is one of only 16 to have received a grant

in 2003 from the Multidisciplinary University Research

Initiative (MURI) program. Sponsored by the Department

of Defense, the MURI program is designed to encourage

the development of multidisciplinary teams from several

universities whose efforts address more than one

traditional science and engineering discipline critical to

national defense. Partnering with the University’s Center

for Nano Science and Technology on the MURI project

are the Vision Research Laboratory and the Nonlinear

Electronics Laboratory of the University of California at

Berkeley, the Molecular Vision Laboratory at Harvard

University, the Signal Processing System Design Laboratory

at Notre Dame, and Pázmány Péter Catholic University in

Budapest, Hungary.

Porod and the MURI team are clear; they are not

“inventing” a parallel processing chip. “That’s been done,”

says Porod. “By employing the concept of cellular

neural/nonlinear networks, image acquisition and data

processing on the same chip at the same time has already

been accomplished by researchers other than those at

Notre Dame. The challenge with the most recent generation

of parallel processing chips, and the problem we are

addressing, is that it is difficult for the current chips to

‘see’ different colors at high speeds. Another concern is

that they can’t detect infrared light, which is useful in a

variety of applications.”

According to Yih-Fang Huang, professor and chair

of the Department of Electrical Engineering, a number

of systems — including target detection, navigation,

tracking, and robotics — rely upon information beyond the

visible spectrum, such as ultraviolet rays, infrared rays,

and radio waves. “The military certainly has a great

interest in detecting infrared light,” says Huang, “but there

are many civilian uses for this research as well, including

law enforcement and medical applications.”

The team describes the project as an example of

the convergence of nanotechnology, biotechnology, and

information technology, but it is more importantly a project

designed to solve a vision problem: developing sensors for

parallel processing chips that will detect infrared light,

which is why the team is modeling the connections within

the eye.

A mammalian retina contains millions of light-

sensitive cells called rods and cones. Rods are sensitive to

dim light but cannot distinguish wavelengths. Cones come

in three types, which respond to short, middle, and long

wavelengths, respectively. All of the cones are used to

capture light, after which electrical signals are sent to the

brain, where they are organized and interpreted as images.

“Obviously, the eye cannot sense infrared light,” says

Patrick J. Fay, associate professor of electrical

engineering, “but because of the way it works, it makes

great sense to use the eye as a model for the development

of vision chips with nanoscale multispectral sensors.”

“Using nanotechnologies such as electron beam

lithography, atomic force microscopy, and scanning-

tunneling microscopy,” says Gary H. Bernstein, “we can

fabricate these bio-inspired sensors so that they function

comparably to the cones in a retina.” Then the sensors,

tens of thousands of nanoscale antennae, will be placed

on a silicon chip to assist in the acquisition and processing

of infrared images.

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A multidisciplinary effort, the Center forNano Science and Technology brings togetherfaculty from many departments acrosscampus. They include:

Department of Electrical EngineeringGary H. Bernstein, professorArpad Csurgay, visiting facultyPatrick J. Fay, associate professorDouglas C. Hall, associate professorDebdeep Jena, assistant professorThomas H. Kosel, associate professorCraig S. Lent, professorJames L. Merz, professorAlexander Mintairov, research facultyAlexei Orlov, research facultyWolfgang Porod, center director and

Freimann Professor Alan C. Seabaugh, associate director of the

center and professorGregory L. Snider, associate professorHuili (Grace) Xing, assistant professor

Department of Chemical and BiomolecularEngineering

Agnes E. Ostafin, assistant professor

Department of Chemistry and BiochemistryThomas P. Fehlner, Grace-Rupley ProfessorHolly V. Goodson, assistant professorGregory V. Hartland, associate professorPaul W. Huber, professorMarya Lieberman, associate professorOlaf Wiest, associate professor

Department of Computer Science andEngineering

Jay B. Brockman, associate professorJesus A. Izaguirre, assistant professorPeter M. Kogge, Ted H. McCourtney Professor

Department of PhysicsMalgorzata Dobrowolska-Furdyna, professorJacek Furdyna, professorBoldizsar Janko, assistant professor

For more information on the center, itsfacilities, personnel, and researchinitiatives, visit www.nd.edu/~ndnano.

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Although hundreds of security efforts have

risen in the wake of 9-11, this particular project

of Alan C. Seabaugh, professor of electrical

engineering and associate director of the Center

for Nano Science and Technology, began with

a call for proposals in 1999, when the United

Engineering Foundation requested papers on

the development of anti-terrorist technology.

Seabaugh’s idea was one of the four selected

from a total of 920 proposals. His concept

focused on the creation of a handheld biotoxin

analyzer that could be used at potentially

contaminated sites, such as the aftermath of

a terrorist attack or an industrial accident.

Instead of using a light source to illuminate

a toxin, which is a traditional way of “seeing”

dangerous substances, Seabaugh’s expertise in

nanoelectronics led him to suggest using

microwave reflection. The use of microwaves

would provide the same accurate measure-

ments as the typical optical method but

allow the finished device to be much

smaller than other devices, possi-

bly the size of a credit card.

Working with graduate students Wei Zhao,

Srivatsan Srinivasan, and Qing Liu, Seabaugh

designed a semiconductor chip that featured

micromachined silicon waveguides through

which fluids would travel. The same channels

that conducted the fluid would guide the elec-

tromagnetic waves.

Completing the requirements for the origi-

nal proposal in June 2004, Seabaugh and his

team demonstrated a prototype of the concept.

“The next step ... whether planning to use this

device as an attack detector or as a medical

diagnostic device,” says Seabaugh, “is to

develop microwave tags for specific toxins or

chemicals and create a database on the chip

for each of those toxins. This type of device

could eventually assist in the safe and targeted

deployment of personnel and resources to

specific sites with detailed information about

the type and level of toxin involved. It could

make emergency efforts much more effective.”

8For more information on the biotoxin analyzer, visit www.nd.edu/~nano/projects/chembio.html.

Alan C. Seabaugh, professor of electrical engineering, and stu-dents received a grant from the United Engineering Foundationfor the development of a handheld toxin analyzer. The proposal submitted in response to a call for anti-terrorist technology was one of only four funded by the foundation.

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8For more information on the microsonic anemometer, visit www.nd.edu/~ame/facultystaff/Morris,Scott.html.

Aerospace engineers track the wind and meas-

ure its velocity as it whips through cities. In

today’s environment, city officials and emer-

gency teams also need this type of information

... to predict the path of pollutants and assess

their toxicity.

An ultrasonic anemometer is a device that is

currently used to provide three-dimensional

wind measurements. But the anemometers

available today are too large to obtain the

small-scale measurements of velocity and

temperature that would be required for many

fluid dynamics and security applications. For

this reason Scott C. Morris, assistant professor

of aerospace and mechanical engineering, is

developing the first microsonic anemometer.

Morris’ microsonic anemometer, proposed

to be less than 1/30 the size of current devices,

will record turbulent flows with up to 60 times

the resolution of other anemometers. This will

provide better information for the modeling of

air flows and chemical dispersion throughout a

city. “For example,” says Morris, “a chemical

detector on a roof top may alert officials to

danger, but alone it cannot provide informa-

tion on where a toxin came from or predict

where it’s going. The effective modeling of

cityscapes, using the information provided by a

series of microsonic anemometers, would offer

the predictive capability necessary to ensure the

safety of a city’s inhabitants.”

Morris is working with Gary

H. Bernstein, professor of electrical

engineering and expert in nanolithogra-

phy, who will fabricate the capacitor micro-

machined ultrasonic transducer (CMUT)

portion of the anemometer with a 30-micron

diameter, the width of a human hair. He has

also developed a relationship with a dispersion

modeling team from the University of Utah

that will assist in the testing phase of the

project.

Once produced, Morris envisions testing the

anemometer with its CMUT probe in places

like Oklahoma City, where officials have

already instrumented the city with ultrasonic

anemometers. According to Morris, “Oklahoma

City is an ideal location because it’s flat. We

can measure the approach of the wind, its

velocity, and its path very easily. And, because

of their smaller size, officials could economic-

ally place more of the microsonic devices

throughout the city to obtain more data.”

The microsonic anemometer proposed by Scott C. Morris,assistant professor of aerospace and mechanical engineering,will be 1/30 the size of currently available ultrasonic devices.

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In addition to working on drug-delivery and

diagnostic devices, Ostafin is collaborating with

Jeffrey W. Talley, assistant professor of civil

engineering and geological sciences; Michael

D. Lemmon, professor of electrical engineer-

ing; Patricia A. Maurice, professor of civil

engineering and geological sciences and direc-

tor of the Center for Environmental Science

and Technology; and Lloyd H. Ketchum,

associate professor of civil engineering and

geological sciences, on an environmental

sewage treatment project.

“In most major cities in the midwest and

northeastern parts of the country, and on the

west coast,” says Talley, “combined sewer over-

flow (CSO) is an important challenge.” In

these cities storm and sanitary sewers are often

connected, so when there’s a storm, raw sewage

and storm runoff can mix together. Cities

usually divert the excess sewage into an open

stream or river, but because it is untreated, this

poses a threat to public health. The team has

proposed using an embedded wireless sensor

network to detect and control the CSO

problem.

As part of a recently funded recommenda-

tion to the Indiana 21st Century Research &

Technology Fund, Talley and team will develop

the network of embedded microprocessors

using off-the-shelf components, EmNet. The

network would supply data in real-time to a

main base which would monitor the sewer

infrastructure in municipalities and provide

data that could be used to design additional

remediation strategies.

Ostafin’s role in the project is to help the

team design sensors that would attach to the

microprocessors. “It’s a challenge,” says Ostafin,

“because it offers a different scale of detection.

In many of the other projects we’re working on,

we are concerned with detecting one chemical

or type of bacteria. In this case, there will be

many types of bacteria ... good and bad ...

floating through the system. Our challenge is to

be able to detect specific types of bacteria with-

out swamping the sensor.” Other challenges

include the fact that the sensors must be

strong, yet almost disposable, and able to with-

stand six to 12 months in a sewer. They must

also be lightweight and very sensitive.

8For more information on the environmental remediation effortsinvolving biosensors, visit www.nd.edu/~cest.

They may not be as humorous as

David Letterman’s Top 10, but these

engineering achievements have literally

changed the world. According to the

National Academy of Engineering, the

20 most significant accomplishments of

the last century were:

1. Electrification

2. Automobile

3. Airplane

4. Water supply and distribution

5. Electronics

6. Radio and television

7. Agricultural mechanization

8. Computers

9. Telephone

10. Air conditioning and refrigeration

11. Highways

12. Spacecraft

13. Internet

14. Imaging

15. Household appliances

16. Health technologies

17. Petroleum and petrochemical

technologies

18. Laser and fiber optics

19. Nuclear technologies

20. High-performance materials

As far-reaching as past achievements

have proven to be, the integration of

nano- and biotechnologies holds even

greater promise in the way it will affect

life in the 21st century.

GreatestEngineeringAchievements ofthe 20th Century

11

There are many examples of biologically

inspired efforts within the College of

Engineering that are being addressed on

the nanoscale. In fact, since nanotechnology

operates on the molecular scale, and molecules

are the building blocks of both biological and

inert matter, it shouldn’t be surprising that one

of the most exciting new fields of study today

combines nanoscience and biotechnology.

Thoreau was right when he said, “The

newest is but the oldest made visible ...” These

“building blocks” are not new at all. What is

new, and what will continue to evolve, is the

way in which researchers are viewing these

formerly invisible particles of matter ... to see

beyond what has been and then apply their

newfound knowledge to make a difference in

the way people live.

Graduate student Tim Ruggaber calibrates probes in prepara-tion for their implementation into the embedded sensor network, EmNet, a project recently funded by the Indiana 21stCentury Research & Technology Fund. Ruggaber is workingwith Jeffrey W. Talley, assistant professor of civil engineeringand geological sciences. The initial stages of this work will beaccomplished in the Hazardous Waste Research Laboratory.

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13

hen Walt Disney introduced

“it’s a small world,” it was

part of the Pepsi-Cola exhibit

at the 1964 World’s Fair.

Located at Flushing Meadows

Park in Queens, New York,

the fair featured more than

140 pavilions on 646 acres and offered dual

themes: “Peace through Understanding” and

“Man’s Achievements on a Shrinking Globe in

an Expanding Universe.” Anyone who attended

the 1964 fair and everyone who’s ever taken a

child to a Disney park knows the “small world”

song. One of its most memorable phrases is,

“There’s so much that we share that it’s

time we’re aware; it’s a small world

after all.” In those words songwrit-

ers Richard M. and Robert B.

Sherman captured the essence

of Disney’s vision for the

exhibit and one of the fair’s

themes. Forty years later,

“it’s a small world” still

emphasizes the similarities

that people around the world

share, the things that make individ-

uals from diverse countries and cultures

more alike than different.

what is sure, at least to faculty in the College of Engineering at the University of

Notre Dame, other engineering educators, and corporations across the country, is that the way engineering is taught

must change if today’s undergraduates are to become more than bystanders in the technological advances of the

21st century. If they are to be leaders in the development of emerging technologies in the 21st century, they must

understand and be able to incorporate the life sciences into their engineering activities.

To the faculty in the College of Engineering,

there is an even more basic denominator, one

commonality that must be explored and taught

at the undergraduate level if the world is to

continue to see the kind of technological

progress in the 21st century that it witnessed

throughout the 20th: life. Every living organism

employs similar biological processes to create

and sustain life. Better understanding the

molecular biology of those processes, being

able to track them, model them, and some day

duplicate them, will enhance the quality of life

for all the inhabitants of this “shrinking globe.”

Although the future is never certain,

w

Photo courtesy of The W

alt Disney

Com

pany

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What James D. Watson

and Francis H.C. Crick

found as they researched, and eventually

solved, the structure of deoxyribonucleic

acid (DNA) was that “the secret of life is

complementarity.” Ironically, it was as true

of their collaboration as it was of the double

helix design they unveiled in 1953. Their

teamwork, as one colleague put it, was “that of resonance between

two minds — that high state in which 1 plus 1 does not equal 2 but

more like 10.”

They shared, as Crick said, “a mad keen to solve the problem

(the DNA structure).” The complementarity they discovered between

the adenine-thymine pair and guanine-cytosine pair in the DNA

ladder echoed the synergy of their partnership. For example,

although Crick championed the complementarity concept, it was

Watson who fit the final pieces of the puzzle together. When outlining

their findings in the journal Nature, they were also in agreement as

to whose name would come first — a flip of a coin was to determine

the order. Finally, in closing that first groundbreaking article,

Watson and Crick served up a British understatement that was

complementary to their well-known brashness. They wrote, “It has

not escaped our notice that the specific pairing we have postulated

immediately suggests a possible copying mechanism for the genetic

material.”

Their discovery, one of the most significant scientific

breakthroughs of the 20th century, opened the door for a better

understanding of the interactions between molecules in living

systems and, thus, a better understanding of life. In 1962 Watson

and Crick received the Nobel Prize in Physiology or Medicine “for

their discoveries concerning the molecular structure of nucleic

acids and its significance for information transfer in living material.”

They shared the honor with Maurice Wilkins of London University.

After their discovery, Watson joined the faculty of Harvard

University and then accepted a position first as associate director

and then as director of the National Institute of Health’s fledgling

Human Genome Project. In 1992 he joined the Cold Harbor

Laboratory in Cold Harbor Spring, N.Y. Today, he is chancellor of

the Watson School of Biological Sciences at the laboratory. Crick

focused his efforts on the synthesis of proteins and the genetic code

as a fellow at the Salk Institute for Biological Studies in San Diego,

Calif. He served as the Distinguished Professor and President

Emeritus of the Kieckhefer Center for Theoretical Biology at the

institute until his death on July 28, 2004.

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The integration of engineering

with life sciences ... from molecular

to ecosystem levels ... is a natural

process. As society’s innovators

engineers have always been the

“builders,” the ones who say “what

if” and then work to make a product, service, or situ-

ation better. At times that means advancing existing

technologies to better meet a need. Often it means

pioneering new technologies.

Some may argue that with the cracking of the

structure of deoxyribonucleic acid (DNA) in 1953 by

James D. Watson and Francis H.C. Crick, the field of

molecular (or cellular) biology is hardly new. Others

would counter that the most dramatic benefits of

that particular achievement are yet to come and that

the leaders of the next technological revolution will

be today’s engineering undergraduates as they

explore and define the field of bioengineering.

“Molecular biology,” says Mark J. McCready,

chair of the Department of Chemical and

Biomolecular Engineering, “is one of the most

profound revolutions in science and technology in

the last 20 years. Two decades ago you couldn’t

effectively engineer the life sciences, because you

couldn’t write equations to accurately describe the

fundamental processes of living systems. It’s only

been in the last 20 years that engineers and biolo-

gists have been able to quantify events at the

cellular level.”

This understanding of living organisms and the

chemical operations that sustain life is pivotal to

being able to engineer biological solutions for a

variety of applications, including medical diagnos-

tics; pharmaceuticals and drug-delivery methods;

“biological” tissue for organ implants; natural

resource conservation; water quality and treatment;

soil enrichment; forest management; food growth,

safety, and preservation; and biodegradable

products. The number and scope of

possible applications are as varied as

the spectrum of life.

Yet, most engineering programs

do not require its students to take

biology courses. In fact, the

Massachusetts Institute of

Technology may be the only other

university in the country that

requires all of its engineering stu-

dents to take a chemical biology

course.

“Before researching ways to inte-

grate biology into our engineering curriculum, we

formed a faculty committee,” says McCready. The

curriculum committee — Jesus A. Izaguirre, assis-

tant professor of computer science and engineering;

Agnes E. Ostafin, assistant professor of chemical

and biomolecular engineering; Glen L. Niebur, assis-

tant professor of aerospace and mechanical engineer-

ing; Ken D. Sauer, associate professor of electrical

engineering; and Jeffrey W. Talley, assistant professor

of civil engineering and geological sciences — found

that a few institutions had been modifying their

chemistry courses to include aspects of chemical

biology, but only for chemical and biomedical

engineering majors.

“We didn’t want to cut chemistry completely;

it’s a fundamental aspect of engineering,” says

McCready. “On the other hand, we believed there

was a distinct advantage in requiring all engineering

undergraduates to experience a course in molecular

biology. And, we’re confident that the chemistry-

molecular biology sequence we have designed, like

our engineering business program, will differentiate

our graduates from students at other institutions.”

The new year-long sequence requires undergradu-

ates to take a traditional course in chemistry during

the first semester of the freshman year. The molecu-

lar biology course is offered during second semester.

Working closely with McCready to develop the

second course in the sequence were A. Graham

Lappin, professor of chemistry and biochemistry,

and Francis J. Castellino, the Kleiderer-Pezold

Professor of Chemistry and Biochemistry and

Director of the W.M. Keck Center for Transgene

Research. “Faculty in chemistry and

biochemistry were instrumental in

helping us achieve our goals,” says

McCready. “Frank Castellino, in

particular, developed an incredible

course for our students that will

give them a solid grounding in

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the biological sciences.”

“Because the basic biological

processes in all organisms are pretty

much identical,” says Castellino, “I

structured the class to emphasize the

unity of chemical, physical, and bio-

logical sciences.” In the course the evolution and

assembly of macromolecules into cellular structures,

as well as the interactions among cells, is stressed.

Throughout the semester, students study the origins

of matter. They learn the basic structure of the

nucleus, as well as nucleosynthesis. They follow

the synthesis of heavy elements and are introduced

to stable and unstable nuclei and nuclear processes

in various radioactive emissions.

Students review human pathologies, from the

natural radioactivity of potassium to the variety of

synthetic nuclides and how they are prepared and

used in the diagnostic and therapeutic applications

of nuclear medicine. They track the evolution of

simple biologically relevant compounds and carbon

bonding.

Castellino also introduces protein, DNA, and

membrane structures to students. They review pro-

tein folding and discuss the roles of simple sugars

and polysaccharides in the transport, structure, and

storage of carbohydrates. Energy storage and the

structure and functions of lipids are also studied.

As the course progresses, students learn the

principles of pathogenesis and host-defense mecha-

nisms, including chemical intervention for the

elimination of pathogens and the development of

antibiotic resistance. They study membrane fusion,

as well as passive and active diffusion — mecha-

nisms for the transport of materials into and out of

cells. The transduction of sensory signals and the

properties of the synapse are also covered, as are

the characteristics of enzymes, enzyme inhibitors,

and the properties of chromosomes.

Largely a lecture course, students

have ample opportunity to debate

the social and ethical issues that

have followed the Human Genome

Project and DNA replication.

“What’s most important,” says

McCready, “is that through this

course, our students begin to under-

stand life science fundamentals in

terms of living systems. Engineering

has always been effective at describ-

ing and designing systems. By estab-

lishing this link early in our

curriculum, our students can build on it throughout

their time at Notre Dame and see how the life sci-

ences connect with the full range of subjects that

they study.”

McCready believes that this “bio” revolution,

especially in the field of health care, is where the

next wave of engineering undergraduates will make

the largest contributions. “Engineers have created

many products and processes that have had a pro-

found impact on health care — such as drug-delivery

patches and insulin pumps — but many of the

developments did not rely on molecular biology.

What if someone said, ’We want an artificial

pancreas’? Engineers would need to develop ways

to sense glucose levels, create a reservoir — with a

means of filling it, and release insulin into the body

without killing the patient. Or what about an artifi-

cial liver? Or a new heart, not just a mechanical

pump but actual biological tissue? The point is that

engineers will significantly drive the ‘bio’ revolution,

but they cannot do so without first

understanding biology. This

course sequence is their

introduction.”

The College of

Engineering also offers addi-

tional courses as electives, as

well as a variety of opportuni-

ties for undergraduate research in

bioengineering activities.

According to McCready, the goal of the

chemistry-molecular biology course sequence is

not to lay the foundation for a degree program in

“bioengineering” at Notre Dame.

Its purpose is to better prepare

engineering undergraduates to be

the leaders and innovators of tomor-

row, so that they can build a better

world ... big or small.

17

Students in the Class of 2007 were the first engineering

undergraduates required to take the new course, Molecular Biology

for Engineers. Nathan Stober, a chemical engineering student from

Granger, Ind., says,“The course gave me insight into how

biological and even nuclear processes are related

to chemical reactions. It also gave me an

introduction to the everyday functions of

cells.”

Stober describes the course as

fast-paced but very interesting. “The most

important thing I learned from the course

and Dr. Castellino [the course instructor],” he

says, “was that a basic knowledge of chemistry is

crucial to the study of almost all engineering, scientific,

or medical fields.”

In addition to providing a strong base in biology for

undergraduates, Molecular Biology for Engineers is proving to be

a stepping stone to the wide range of bioengineering research

opportunities offered throughout the College of Engineering for

these first-year students, who would not normally have the

opportunity to participate in hands-on research until the end

of their sophomore year.

Ailis Tweed-Kent, a classmate of Stober’s and native of

Pittsfield, Mass., is applying the knowledge she gained in the course

to her work in the Tissue Culture Laboratory. Under the direction of

Agnes E. Ostafin, assistant professor of chemical and biomolecular

engineering, Tweed-Kent is studying osteoblasts, the bone cells

responsible for producing calcium. “The work I’m doing here is

the first step in the research process,” she says. “By observing

the morphology of the cells and

using chemical assays, we

can gather information

on their activity.

When we have a

basic understanding

of how the cells

function, then we can

move to the next step

in the process.”

Nathan Stober

Ailis Tweed-Kent

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Consider the impact they

have had to date. Engineers

are the dreamers and the

doers. They apply the “what ifs” and make them practical

and effective for commercialization. For example, at the

dawn of the Industrial Revolution, engineers took the

concept of power-driven machinery and set it into motion

for manufacturing. In the race for space, they employed

their ingenuity not only to send men and machines to the

moon, but they also extended space technology to the

development of hundreds of products — from wireless

phones and heart pumps to the creation of new metal

alloys and lightweight composite materials. It’s called

technology transfer, and it’s the process through which the

impact of research and development on the marketplace is

maximized.

While organizations like the National Academy of

Engineering (NAE), Honeywell International, NEC Foundation

of America, National Science Foundation (NSF), and SBC

Foundation believe that the engineers of tomorrow will

continue to identify problems and find solutions — many

of which will be commercialized — they are also

What role will engineersplay in the future?

19

The NAE, NSF, Honeywell, NEC, and SBC are not the

only participants in the discussion about the future of

engineering education. According to Arthur T. Johnson,

professor of biological resources engineering at the

University of Maryland and author of a book and several

papers on biology for engineers, “the frantic rush to

establish and enhance academic bioengineering programs

in the United States ... may also have kept bioengineering

from emerging in an orderly and thoughtful way.”

What exactly is “bioengineering”? It’s been defined

by a number of people in a variety of ways. Some view it

as specifically applying to medicine and health care.

Others describe it as anything affecting the human

organism. The National Institutes of Health defines

bioengineering as “an integration of the physical,

chemical, or mathematical sciences and engineering

principles for the study of biology, medicine, behavior,

or health. It advances fundamental concepts, creating

knowledge from the molecular to the organ systems level.

It develops innovative biologies, materials, processes,

implants, devices, and informatics approaches for the

prevention, diagnosis, and treatment of disease; for patient

rehabilitation; and for improving health.” But biology

also affects ecology and the environment. In fact, it is

the impetus for a multitude of bio-inspired research

projects across numerous fields.

Johnson believes that “all engineers these days

should know something about biology.” They should have

a broad understanding of biological principles, be able

to apply the information known about “familiar living

systems” to those of less familiar or unknown systems.

They also need to be willing to work in collaborative teams,

whose members offer a variety of skills and approaches.

His recommendation for a successful undergraduate

engineering curriculum is one that offers “basic

instruction in physics, mathematics, chemistry, biology,

and engineering. Students should be able to view the

full horizon of potential biological applications, from

subcellular to ecological levels.” This corresponds to

the approach the College of Engineering has taken in

developing its new chemistry-molecular biology course

sequence for undergraduates.

sponsoring a two-phase initiative to identify desired

attributes of engineers in 2020. The purpose of the study

is to suggest strategies

for engineering

education that will

better prepare students

to meet the challenges

of the future.

The attributes

identified by the first

phase of the study

suggest that engineers

must continue to

possess strong

analytical skills and

exhibit practical

ingenuity and creativity.

They will need to

be excellent

communicators who

have mastered the

principles of business management. These leaders must

also adhere to high ethical standards and have a strong

sense of professionalism. Many of these qualities are

evident in today’s engineers. But, what the study has

deemed imperative for future engineers is that they be

lifelong learners who are flexible and innovative. In fact,

according to the study:

“The pace of technological innovation will continue to

be rapid (most likely accelerating). The world in which

technology will be deployed will be intensely globally

interconnected. The population of individuals who

are involved with or affected by technology (e.g.,

designers, manufacturers, distributors, and users) will

be increasingly diverse and multidisciplinary. Social,

cultural, political, and economic forces will continue

to shape and affect the success of technological

innovation. The presence of technology in our

everyday lives will be seamless, transparent, and

more significant than ever.”

As a senior Jonathan Nickels, far left, worked with Andre Palmer, assistantprofessor of chemical and biomolecular engineering, to develop a mechanicallystable liposome, a hollow structure similar to a biological cell. Researchersbelieve that liposomes may offer a less toxic method of drug delivery, as theyare able to target infected cells while leaving healthy tissue in tact. Nickels, nowa graduate student at the University of Texas, demonstrated that the shape andsize of liposomes can be engineered to make them more resilient to the shearforces in the blood stream. He published a paper on his undergraduate workwith Palmer in both the Biophysical Journal and Langmuir.

Sarah Bergler is a senior developmentengineer at Zimmer, Inc. A Double Domer,Bergler received a bachelor’s degree in mechanical engineering in 1994 and amaster’s degree, also in mechanical engi-neering, in 2001. A leader in the design,manufacture, and distribution of orthope-dic implants and fracture managementproducts, Zimmer is located in Warsaw,Ind., less than an hour from Notre Dame.

college news

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College of Engineering Sponsors International Conferences

Many aspects of “academics” make living orworking on or near a campus unique. Inaddition to the special speakers and per-forming arts programs that are offered, uni-versities are places where researchers andother professionals can gather to garnernew ideas for their investigations, as wellas share their findings, in an effort toimprove the overall state of a particularfield. The University of Notre Dame andCollege of Engineering are proud to be partof such efforts and to serve as host formany events, including the following mostrecent conferences:

International Symposium on Flow Visualization

According to Roth-Gibson Professor ofAerospace and Mechanical EngineeringThomas J. Mueller, chairman of the 11th International Symposium on FlowVisualization (ISFV-11), the event — heldon the Notre Dame campus from August 9through August 12, 2004 — went very well.“The symposium originated in 1977,” says

Mueller. “In fact, I went to the first sympo-sium and then became a member of theinternational organizing board, working on following symposia. Our goal was to foster a global forum for communicationand information exchange in the field offlow visualization.”

Recalling the years since the first sym-posium, Mueller stresses that flow visuali-zation has undergone huge changes. Theuse of lasers for illumination and theincreased use of computers for data pro-cessing and computations has led to rapiddevelopment in a number of areas. “Forexample,” says Mueller, “during the firstsymposium, there were no papers on theuse of particle image velocimetry and onlyone or two that featured numerical solu-tions. Our most recent gathering featuredmore papers on these two techniques thanall of the other techniques combined.”

Flow visualization can be applied to avariety of fields such as experimental andcomputational fluid dynamics, aerodynam-ics, mechanical engineering, chemical engineering, civil engineering, metallurgy,

meteorology, oceanography, biomedical,and food and agricultural technology.

The symposium was first hosted by theInstitute of Space and Aeronautical Scienceat the University of Tokyo. Over the years, it has been held in Germany, France, theCzech Republic, Italy, England, and theUnited States. “This is only the third time it has been held in the U.S.,” says Mueller,“and the first time it’s been at Notre Dame,even though the University has a long history in flow visualization.”

For more information on ISFV-11, visitwww.ode-web.demon.co.uk/11isfv. For information on the history of flow visualization at Notre Dame, visitwww.nd.edu/~ame.

LaVision, Inc., is an international company specializingin imaging solutions, specifically CCD-based cameraand integrated optical diagnostics systems in the fieldof fluid dynamics. It was one of the exhibitors at the11th International Symposium on Flow Visualization,held at the University of Notre Dame in August 2004.Representatives from LaVision’s North Americansubsidiary in Ypsilanti, Mich., above, demonstrate aparticle image velocimetry system using a free jet.

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Ethics and Changing Energy Markets: Issues for Engineers, Managers, and Regulators

Sponsored by the University of Notre Dameand Carnegie Mellon University, the firstconference on Ethics and Changing EnergyMarkets: Issues for Engineers, Managers,and Regulators (EnergyEthics 2004) isscheduled for October 28 - 29, approxi-mately 14 months after the largest blackoutin the history of North America. Accordingto the Michigan Public Service Commission’sReport, “The August 14th blackout was awake-up call concerning the reliability ofour nation’s electric grid.”

But the fact is that consumer confidencewas already shaky long before approxi-mately 50 million people — from south-eastern Michigan through Ontario andnorthern Ohio, all the way east to New YorkCity — found themselves without electrici-ty. People around the country had ques-tions about Enron, they were worried aboutthe California energy crisis, and they wereconcerned about the future of the energyindustry.

EnergyEthics 2004 is the first conferenceto convene energy experts and industryleaders in order to engage them in discus-sions of ethical, market, and regulatoryissues as they pertain to energy generationand use. Some of the topics to be coveredat the conference include the roles of engi-neers, managers, and regulators in estab-lishing an operational framework that isresponsive to the market as well as to theneeds of consumers.

Featured speakers — from the energyindustry, regulatory agencies, and academia— will explore the issues arising in the shiftfrom regulated to competitive markets anddiscuss the historical applications of energyin today’s market. They include theHonorable Patrick Wood III, chairman of the Federal Energy Regulatory Commission;Vernon L. Smith, a Nobel Laureate inEconomics and professor of economics and law at George Mason University;Bethany McLean, a writer for FortuneMagazine and co-author of “The SmartestGuys in the Room”; and Vicky Bailey, apartner with Johnston & Associates and former assistant secretary of energy forPolicy & Intergovernmental Affairs of theDepartment of Energy.

Frank P. Incropera, the McCloskeyDean of Engineering at Notre Dame; IndiraNair, the vice provost for education atCarnegie Mellon University; PatrickMurphy, professor of marketing at theUniversity and the Smith Co-director of theInstitute for Ethical Business WorldWide;and Notre Dame alum Anthony F. EarleyJr., chief executive officer of DTE Energy, will also be speaking.

For more information about this conference,visit energyethics2004.nd.edu.

The use of water to study fluid flow dates back toLeonardo da Vinci, the Renaissance engineer, architect,painter, and sculptor. More recently, water tunnels havebeen used to study the complex interactions of flow onaircraft shapes. The water table shown here, exhibitedat the 11th International Symposium on FlowVisualization by Rolling Hills Research Corporation in El Segundo, Calif., uses dye injection to visualizeleading-edge vortices on a delta wing.

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Teacher of the YearSince joining the University in 1990, Joannes J. Westerink, associate professor in theDepartment of Civil Engineering and Geological Sciences and director of the EnvironmentalHydraulics Laboratory, has earned many accolades for his personable and approachable

teaching style. Students describe him as a teacher who is “patient, laid-back, and easy to talk to.” Theyacknowledge that his classes are demanding, but theyalso say, “He is interested in getting to know us on apersonal level and wants us to get the best out of hiscourses.”

Westerink’s passion for his field, something students also comment upon, honors a long-standing

tradition within the College of Engineering, as a civil engineering program has been offered at Notre Dame since 1873.

College Selects Kaneb HonoreesThe Kaneb Teaching Awards are bestowedannually on faculty who have been activein full-time undergraduate teaching for aminimum of five years. Nominees are cho-sen based upon the recommendations ofcurrent students, recent graduates, and fellow faculty. This year’s recipients wereDanny Z. Chen, professor of computer science and engineering; David T. LeightonJr., professor of chemical and biomolecularengineering; Robert C. Nelson, professor ofaerospace and mechanical engineering;Stephen E. Silliman, professor of civil engi-neering and geological sciences and associ-ate dean for educational programs; GregoryL. Snider, associate professor of electricalengineering; and Robert A. Howland, associate professor of aerospace andmechanical engineering.

Chen has developed a reputation forexcellence in the classroom, and studentsconsistently rate his Analysis of Algorithmscourse in the upper quartile of classestaught within the Department of ComputerScience and Engineering. He joined theUniversity in 1992.

According to students, Leighton offers“interesting and insightful class demonstra-tions, but he also makes himself availableoutside of class.” Leighton has been a faculty member since 1986.

David T. Leighton Jr.

Joannes J. Westerink

T H E F I R S T O U T S T A N D I N G

T E A C H E R O F T H E Y E A R

A W A R D W A S P R E S E N T E D

I N 1 9 7 7 .

Nelson has been recognized for hisefforts in a number of courses since joiningthe University in 1975, but students comment most about his approach toAerodynamics Laboratory, one of the mostdemanding in the aerospace engineeringprogram.

Since 1986 undergraduates in both theenvironmental geosciences and civil engi-neering programs have experienced theenthusiasm and hands-on approach toengineering applica-tions displayed bySilliman.

Snider has devel-oped the IntegratedCircuits laboratorycourse into a one-of-a-kind fabricationexperience in siliconcircuitry for under-graduates. They leavethe course with a definite advantage overtheir electrical engineering peers at otherinstitutions. Snider joined the University in 1994.

A faculty member since 1981, Howlandhas consistently been cited for his ability toexplain difficult concepts and the enthusi-asm with which he presents the material. Asone student said, “He is the most challeng-ing professor I have, but he also puts in theextra effort to make sure students have theopportunity to learn.”

C R E A T E D I N 1 9 9 9 T H R O U G H

A G I F T F R O M U N I V E R S I T Y T R U S T E E

J O H N A . K A N E B , T H E K A N E B T E A C H I N G

A W A R D S H O N O R F A C U L T Y F O R T H E I R

“ O U T S T A N D I N G S E R V I C E A S

E D U C A T O R S . ”

Robert C. Nelson Stephen E. SillimanDanny Z. Chen

Gregory L. Snider

Robert A. Howland

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Distinguished Engineering Lecture Series Begins Fifth Year The Distinguished Engineering Lecture Series, established in 2000 by Dean Frank P. Incropera,is entering its fifth year of service to undergraduates. Its goal is to expose students, particular-ly first-year engineering intents, to professional engineers who have achieved at the highestlevels in their fields, giving the new undergraduates an overview of the range of opportunities

available in engineering and providing them with a deeper understand-ing of the role of engineering in society and the impact that they, asfuture engineers, can have. The two speakers who participated this pastyear represent different fields, but they both serve in high-profile indus-tries where decisions and actions can have tremendous consequences.

William F. Readdy, associate administrator of NASA’s Office ofSpace Flight, delivered the first talk in the 2003-04 series. A former astronaut and veteran of three space shuttle missions — including commanding a docking mission to the MIR Space Station — he isresponsible for the Johnson, Kennedy, Marshall, and Stennis space stations; the International Space Station; and space shuttle, space communications and space launch vehicles programs.

During his presentation, “Engineering Challenges in Human SpaceFlight: NASA’s Path from Columbia Recovery to Return to Flight,”

Readdy discussed the engineering challenges of space flight as he highlighted the incrediblesuccesses and tragic failures of the space program. He also addressed the Columbia AccidentInvestigation Board report and the path that NASA has chartered for a stronger, smarter, andsafer flight program.

Readdy earned a bachelor’s degree in aerospace engineering, withhonors, from the U.S. Naval Academy and is a distinguished graduate ofthe U.S. Naval Test Pilot School.

The second speaker in the 2003-04 series was Michael O’Sullivan,senior vice president of development for FPL Energy, LLC. His talk,“Engineering Careers and the Energy Industry,” outlined the importanceof energy in a global economy; wind energy, one of the most excitingdevelopments in power generation today; and the benefits of an engineering education.

O’Sullivan, who was appointed to his current position in July 2001, is responsible for FPL Energy’s business development and asset acquisition activities. He previously held management positions atCommonwealth Edison, NRG Energy, and the AES Corporation.

A registered professional engineer, O’Sullivan earned his bachelor’sdegree in civil engineering from Notre Dame in 1982 and a master’s of business administra-tion degree from the University of Chicago in 1987.

FPL Energy is one of the largest providers of clean energy in the United States, operatingfacilities — natural gas, wind, solar, hydroelectric, and nuclear — in more than 20 states.

Speakers for the 2004-05 academic year will be announced on the College of Engineeringhome page, www.nd.edu/~engineer, later this year.

To ProfessorPatrick J. FlynnComputer Science and Engineering

Michael D. LemmonElectrical Engineering

To Associate ProfessorJ. William GoodwineAerospace and Mechanical Engineering

To EmeritusJohn W. LuceyAerospace and Mechanical Engineering

Recognized for 25 Years of ServiceDavid J. KirknerCivil Engineering and Geological Sciences

Roger A. SchmitzChemical and Biomolecular Engineering

faculty promotions

Michael O’Sullivan

William F. Readdy

department news

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Seniors Test Their WingsEach spring aerospace engineering seniors are required to participate in a capstonedesign course. According to instructor Thomas C. Corke, the Clark Equipment Professor of Aerospace and Mechanical Engineering, the purpose of the course is to give students ahands-on design experience. By working through the various steps of the design process,students learn the use of constraints; they come to understand the interactions betweencompeting technologies; and they develop an appreciation for the roles of planning andcommunication. “Consequences are not as critical in a senior design course as they wouldbe in the real world,” says Stephen M. Batill, professor and chair of the Department ofAerospace and Mechanical Engineering, “but the skill set our students gain from thisexperience is priceless. It makes a difference in their effectiveness as professionalengineers.”

This year the challenge was to design and build a remote piloted aircraft which couldcarry a specified payload, take-off on grass in less than 300 ft., and land safely. Althoughstudents who had experience building model aircraft or working with electronics mayhave held a slight advantage, each team was required to use the same equipment and fol-low specific design parameters: Planes were required to feature a fixed main wing, housean electric motor and battery power pack, and carry an internal cargo which included a“sport” propeller, an on-board microprocessor, and a digital radio control system that featured a minimum of seven channels.

Student teams worked throughout the semester, first creating the “paper” design of theplane and then making a formal presentation to the rest of the class on their vehicles andtheir predicted performance. Next, teams developed a full set of CAD-CAM drawings,including details of individual components. Parts they could not purchase were manufac-tured by the students in the aerospace engineering laboratories.

Flight tests were held at theSouth Bend Model Aircraft Club fly-ing field, approximately 30 minutesfrom the Notre Dame campus. Eachteam’s aircraft was required to main-tain a specific velocity at a constantaltitude and also achieve a changein altitude through a minimum of a100-ft. climb. During the flight test,the microprocessor aboard eachplane transmitted informationregarding the velocity and altitudeof the aircraft to a laptop computerlocated on the ground.

Students analyzed this information and included it in their final presentations, whichwere made to classmates and an industry panel. Panel participants were Daniel T.Jensen, a senior project engineer for the Rolls-Royce Corporation who received a master’sdegree in mechanical engineering from Notre Dame in 1990; Gregory Addington, aresearch aerospace engineer at the Air Force Research Laboratory who received a master’sdegree in mechanical engineering from the University in 1996 and a doctorate in 1998;Frank C. Berrier and Christian V. Rice of the Boeing Corporation; and Steven Eno of theHoneywell Corporation.

Mechanical engineering students are also required to participate in a senior designcourse. It is typically offered during the fall semester.

For more information on the senior aircraft design course and to view flights of each team’s aircraft, visit http://www.nd.edu/~engineer/ame441.

Mueller Named AIAA FellowThe American Institute of Aeronautics andAstronautics (AIAA) has named Thomas J.Mueller, the Roth-Gibson Professor ofAerospace and Mechanical Engineering, a Fellow in Aerospace Sciences.

Mueller is a leading researcher in the complex flow phenomena present at lowReynolds numbers and is well known bythe aeroacoustics community as an excep-tional experimentalist who has made significant contributions to his field.

The author and co-author of severalbooks and numerous journal articles,Mueller also served as director of engineering research and graduate studiesfrom 1985 to 1989 and as chair of theDepartment of Aerospace and MechanicalEngineering from 1988 to 1996. He joinedthe University in 1965.

Thomas J. Mueller

A E R O S P A C E A N D M E C H A N I C A L E N G I N E E R I N G

h t t p : / / w w w . n d . e d u / ~ a m e

He is the fourth member of theDepartment of Aerospace and MechanicalEngineering to receive this honor: Viola D.Hank Professor Hafiz M. Atassi, ProfessorRobert C. Nelson, and Professor Eric J.Jumper also hold the title of AIAA Fellow.

Professor Thomas C. Corke with Team “HammerHead (H2)”

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Center for Microfluidics and Medical Diagnostics Teams with Industry PartnersIn the September 2004 issue of Business 2.0, an article titled “Seven New Technologies That Change Everything” by G. Pascal Zachary identifies microfluidics as one of the hottestemerging technologies because it offers the potential of eliminating expensive laboratorytests and the lengthy wait for results. According to Zachary, sales of currently availablemicrofluidic test kits are projected to reach $300 million by the end of the year. In fact, saysZachary, the U.S. Postal Service has already installed microfluidic detection systems at majorprocessing centers in an effort to identify anthrax laced mail.

These actions are not surprising to Andrew Downard, product development manager forthe Center for Microfluidics and Medical Diagnostics at Notre Dame. “Microfluidics researchhas been going on for quite awhile,” says Downard. “It’s just a matter of time before it makesthe full-fledged jump from university laboratories to commercial applications, where small,cost-effective test kits could be sold over-the-counter. Bacteria, viral infections, and diseases

such as tuberculosis or SARS ... could be identified quickly and more cost-effectively.”

One of the goals of the center, which was established in 2003, is tofacilitate the type of technology transfer Downard describes. In fact, thecenter is working with Scientific Methods., Inc., of Granger, Ind., on thedevelopment of a portable beach-monitoring sensor that can detect dangerous E. Coli in a matter of minutes. Currently, the decision to closepublic beaches is driven by laboratory tests, which take up to two days to process. Researchers are incorporating a bacteria trap into the hand-held sensor. The trap uses A/C electro-osmotic flow to force bacteria into highly concentrated lines, giving municipal officials real-time information about the water quality to better safeguard public health.

“We’ve been working with Scientific Methods since April 2004,” says Downard, “and it’s been a good match. We have the expertise in fluid mechanics, and they have the expertise in microbiology and business applications.”

According to Downard, the company has also been instrumental inhelping the center with research and development space for Microfluidic Applications (MFA),a separate company founded by faculty within the center. The company serves as an incuba-tor for research projects that offer the best possibilities for commercialization. Personnel inthe company are working with researchers to develop viable products. They are also applyingfor Small Business Innovative Research grants and seeking private-equity investments to fundthese efforts.

One of the devices MFA is developing is a Zetafilter, which will be used for the elec-trophoretic separation and concentration of bacteria, viruses, and proteins. Separation isbased on the size and charge of the molecule, providing faster processing times and moreselectivity than currently available products. Its principal applications will be for medical,proteomic, and environmental researchers. Downard recently completed a working prototypeof the Zetafilter and is currently working to commercialize the technology.

The center director is Hsueh-Chia Chang, the Bayer Professor of Chemical andBiomolecular Engineering. David T. Leighton Jr., professor of chemical and biomolecular engineering, is associate director.

For more information about the center, its faculty, and current projects, visithttp://www.nd.edu/~chegdept/CMMD.html.

C H E M I C A L A N D B I O M O L E C U L A R E N G I N E E R I N G

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Jim Larkin, left, president of ScientificMethods, Inc., of Granger, Ind., discussesthe standard laboratory technique for E. Coli detection with Andrew Downard ofNotre Dame’s Center for Microfluidics andDiagnostics. The current technique takesup to two days to process. Centerresearchers are working with ScientificMethods to develop a portable E. Coli testkit that will give immediate results.

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Brian Bucher, juniorValparaiso University“Determining the Abundance of Platinum Group Elements along Urban Roadsides”

Elizabeth Hernadon, freshmanWashington University“Determining the Reversibility of Bacillus Subtilis Adsorption to Mineral Surfaces”

Todd Hoppe, sophomoreTulsa University“Mercury Speciation and Availability in Tidal Waters, Suspended Solids, and Sediments

from the San Francisco Bay”

Terri Huynh, sophomore University of California at Berkeley“Metal Adsorption onto Bacterial Consortia from Uncontaminated Geologic Settings:

Building Predictive Models”

Nathan Porter, sophomoreUtah State University“Synthesis and Characterization of Uranyl Oxalate Compounds”

Ginger Sigmon, juniorNorth Carolina State University“Uranyl Peroxides”

Rachel Thompson, juniorRockford College“The Effects of Nickel on the Growth of the Aerobic Bacterium Pseudomonas Mendocina”

Petia Tontcheva, juniorUniversity of Illinois at Chicago“The Effects of Water-retention Parameters on Air Entrapment below the Water Table”

Talley Named to Joint ChiefsIn July 2003 Jeffrey W. Talley, assistantprofessor of civil engineering and geologi-cal sciences and colonel in the U.S. ArmyReserve, returned from extended service inOperation Iraqi Freedom. He had spent sixmonths there serving as chief of operationsfor the U.S. Army’s 416th EngineeringCommand. Talley earned the Bronze Starfor his service in Iraq.

Since January 2004 he has been serv-ing as a strategic planner for the War onTerrorism Directorate of the Joint Chiefs ofStaff (JCS), one of a handful of reserve offi-cers who have been appointed to the JCS.

A full-time faculty member, Talley’swork for the Joint Chiefs is conducted dur-ing semester breaks and summer reserveservice. In fact, a good part of this summerhas been spent helping prepare Joint StaffAction Packages, white papers suggestingterrorism policies to JCS Chairman Gen.Richard Meyers, Secretary of DefenseDonald Rumsfeld, and President Bush.

Talley joined the Notre Dame faculty in2001 after earning a doctorate in civil andenvironmental engineering from CarnegieMellon University. He holds three master’sdegrees — in environmental engineering and science from The Johns HopkinsUniversity, in history and philosophy fromWashington University in St. Louis, and inreligious studies from Assumption College.He specializes in the environmentallyfriendly remediation of contaminatedgroundwater, soils, and sediments.

EMSI Offers Outreach ProgramsOne of the goals of the EnvironmentalMolecular Science Institute (EMSI) at NotreDame is to bring engineers and scientiststogether to investigate the interactionbetween microparticles and heavy metalsin the environment.

In addition to its research efforts, EMSIis involved in a variety of educational and outreach programs, one of which is theResearch Experiences for Undergraduates(REU) program. A 10-week summer initia-tive, students participating in the REU program receive hands-on experience in geomicrobiology, environmental mineral-ogy and geochemistry, and hydrology underthe supervision of Notre Dame faculty.During the 2004 session, which ended onAugust 7, the following students participat-ed, each focusing on a particular area ofresearch:

Caleb Laux, a local high school student, receivedsecond place for his work on “The Effects of Aluminumon the Formation of Natural Organic Matter Aggregate.”Much of his work was accomplished in the laboratoriesof the Environmental Molecular Science Institute.

27At the close of the program, REU stu-dents were required to participate in aresearch forum by presenting a 15-minuteseminar on their project followed by aquestion-and-answer period.

The EMSI also hosts a high school out-reach program for area students. This yearstudents from three area high schools —Marian, Clay, and Adams — participated inhands-on projects which were presented at the annual Indiana Regional Science Fair.In fact, four of the students involved, allfrom Marian High School, won prizes at thefair for their efforts: For her project on“Monitoring High Nitrate Levels in Benin,West Africa,” Claire Shearer, a rising senior,won first place in behavioral and social science. She also received the KodakPhotographic Award and the AmericanSociety for Quality Award. Another student,rising senior Caleb Laux received a secondplace award in biochemistry. His project,“The Effects of Aluminum on the Formationof Natural Organic Matter Aggregate,” also

received the second place EnvironmentalManagement Association Award. DeannaLind, a rising freshman, presented “TheEffects of Copper Ions on UV254Measurement for DOC in Water.” Shereceived a first place in chemistry, as well asthe Stockholm Junior Water Prize and theAmerican Society for Quality Award.Margaret Garascia, rising senior, received a first place in chemistry for her project,“Hydrothermal Alteration of Cement and ItsApplication to Nuclear Waste Disposal.”

Although not as formal as the REU and high school outreach programs, EMSIalso sponsors tours and special events forlocal middle schools. For example, inNovember 2003, the EMSI and Center forEnvironmental Science and Technology co-hosted a tour and lecture for 40 studentsfrom The Montessori Academy at EdisonLakes, located in Mishawaka, Ind.Discussions with students included the mission of the institute and how the envi-ronmental research occurring in the EMSIrelates to their lives.

For more information about the research initiatives and outreach programs in theEMSI, visit http://www.nd.edu/~emsi.

C I V I L E N G I N E E R I N G A N D G E O L O G I C A L S C I E N C E S

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Students from The Montessori Academy at Edison Lakes in nearby Mishawaka, Ind., toured the Environmental MolecularScience Institute and the Center for Environmental Science and Technology in November 2003. They used ideas discussed during the tour as the basis for their science fair projects.

Terri Huynh, a molecular biology major at theUniversity of California at Berkeley, participatedin the 2004-05 Research Experiences forUndergraduates Program in the EnvironmentalMolecular Science Institute. Her advisor wasJeremy B. Fein, institute director and professor of civil engineering and geologicalsciences.

Salvati Receives NSF CAREER AwardClare Boothe Luce Assistant Professor LynnA. Salvati has been named a recipient ofthe National Science Foundation’s EarlyCareer Development (CAREER) Award.Salvati, a geotechnical engineer, is receivingthe CAREER award for her proposal titled“Cyclic Behavior of Cemented Sands:Testing, Field Verification, and Modeling.”

The highest honor bestowed by thegovernment on junior faculty, the CAREER program recognizes and supports youngfaculty who exhibit a commitment to pro-viding stimulating research and outstand-ing educational opportunities.

Salvati joined the Department of CivilEngineering and Geological Sciences in2002. She received her bachelor’s degree in civil engineering from Brown Universityand her master’s degree and doctorate in geotechnical engineering from theUniversity of California at Berkeley.

Lynn A. Salvati

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Computational Medicine Group Helps Improve Radiation Therapy Treatment TimeThe goal of researchers and physicians in radiation therapy is to deliver high doses ofradiation to a targeted area while minimizing the damage to surrounding normal tissueand critical organs. One of the current techniques is called intensity-modulated radiationtherapy (IMRT), which requires the ability to generate non-uniform dosages.

Steps taken during a typical IMRT treatment include scanning the area to provide atomographic image of the tumor and surrounding tissue, calculating the dosage based onthe tomography of the tumor, setting the “movements” of the cylinder — a computer-controlled multileaf collimator (MLC) which delivers the beams of radiation, and thendelivering the radiation. The challenge is in generating a plan for the movements of theMLC, because it consists of up to 80 pairs oftungsten leaves which must each be adjust-ed to accurately shape the beam. This iscalled leaf-sequencing, and it is a vital partof the treatment plan as the maximum doserequired must be delivered in the minimum amount of time.

Using new algorithms and computa-tional geometry techniques, theComputational Medicine Group at NotreDame has been developing solutions tothis leaf-sequencing challenge. The team,led by Danny Z. Chen, professor of com-puter science and engineering, includesSharon X. Hu, associate professor of com-puter science and engineering, graduate students Shuang Luan and Chao Want, and former Ph.D. candidate Xiaodong Wu. The Notre Dame team has been collaborating withresearchers in the Department of Radiation Oncology at the University of Maryland Schoolof Medicine, who are performing extensive experimental studies using the new algorithmsand software developed at Notre Dame.

This software, called SLS, produces IMRT plans that compare favorably with the currently available IMRT software, while reducing the time required to establish the plan by approximately two-thirds. As a result, the SLS software is now being used in the University of Maryland Medical Center and the Helen P. Denit Cancer Center inMontgomery General Hospital. Journal papers on the work have been accepted for publi-cation in the Journal of Physics in Medicine and Biology and the Journal of Medical Physics.Research results were also presented at the 45th Annual Meeting and Technical Exhibitionof the American Association of Physicists in Medicine and the 19th ACM (Association forComputing Machinery) Symposium on Computational Geometry.

Intensity-modulated radiation therapy plansgenerated by the new leaf-sequencing softwaredeveloped at Notre Dame may reduce treatment timesby approximately two-thirds.

C O M P U T E R S C I E N C E A N D E N G I N E E R I N G

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Flynn Named Kaneb Faculty FellowPatrick J. Flynn, professor of computer science and engineering, has been named a faculty fellow for 2004-05 by the John A.Kaneb Center for Teaching and Learning.

Established in 1995, the center assistsNotre Dame faculty in evaluating andimproving their teaching abilities as well asincorporating technology into classroomactivities. Each year the center honors outstanding faculty across the University.

One of eight fellows named for the cur-rent academic year, Flynn will join the otherfellows in sharing his teaching experiencesand techniques through a series of work-shops, discussions groups, research projects, and individual consultations.

Flynn received his bachelor’s degree inelectrical engineering, his master’s degreein computer science, and his doctorate incomputer science, all from Michigan StateUniversity.

He co-directs the Computer VisionResearch Laboratory with Kevin W.Bowyer, the Schubmehl-Prein Chair inComputer Science and Engineering.Working with student researchers, theyhave assembled one of the largest and most comprehensive multi-modal biometric

signature databases in the world.

Patrick J. Flynn

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Striegel Receives NSF CAREER AwardAssistant Professor Aaron Striegel has been named a recipient of the National ScienceFoundation’s Early Career Development (CAREER) Award. This is the highest honor given bythe U.S. government to junior faculty in engineering and science.

Established in 1995, the CAREER program recognizes and supports “exceptionally promis-ing college and university junior faculty who are committed to the integration of research andeducation,” says NSF Director Rita R. Colwell. “Its goal is to help top-performing scientists andengineers early in their careers to simultaneously develop their contributions and commit-ment to research and education.”

Striegel joined the Department of Computer Science and Engineering in 2003. He receivedboth his bachelor’s and doctoral degrees in computer engineering from Iowa State University.He is receiving the CAREER award for his work on stealth multicast techniques, titled“Transparent Bandwidth Conservation Techniques.”

Aaron Striegel

Graduate Student Receives Indiana Governor’s AwardDane Wheeler, a Ph.D. candidate and Semiconductor Research Corporation fellow workingunder the direction of Alan C. Seabaugh, professor of electrical engineering, and Douglas C.Hall, associate professor of electrical engineering, has received the 2004 Indiana Governor’sAward for Tomorrow’s Leaders. Wheeler received his bachelor’s degree from the University in 2003. As an undergraduate he won first-place in the Intel Student Research Contest andreceived the award for Best Undergraduate Plan from the Gigot Center for EntrepreneurialStudies at Notre Dame. As a high school student, Wheeler co-developed a software packagecalled mightybrain.com, which enables teachers to record and distribute grades and relevantinformation to students and parents. The program is currently in use at a large local schoolsystem, the Penn-Harris-Madison Corporation, in Mishawaka, Ind.

Dane Wheeler

Fuja Named IEEE FellowThomas E. Fuja, professor of electrical engineering, has been named a Fellow of the Institutefor Electrical and Electronics Engineers (IEEE). The world’s largest technical professional society, the IEEE is composed of more than 320,000 members who focus on advancing the theory and practice of electrical, electronics, and computer engineering. Fuja is the 11th faculty member to receive this honor. His work addresses coding for wireless applications andthe interface between source coding (compression) and channel coding (error control). Hejoined the University in 1998.

Fuja received bachelor’s degrees in electrical and in computer engineering in 1981 fromthe University of Michigan. From Cornell University he received a master’s degree in 1983 anda doctorate in 1987, both in electrical engineering.

Thomas E. Fuja

E L E C T R I C A L E N G I N E E R I N Gh t t p : / / x m l . e e . n d . e d u

University of Notre DameCollege of Engineering257 Fitzpatrick HallNotre Dame, IN 46556-5637

Volume 6, Number 1

Scanning a photograph or slide on a desktop computer and

then printing it on a laser or ink-jet printer produces a

two-dimensional image. It’s flat. Even though it may still

show a stunning subject, there are nuances to the image

that have been lost. These nuances are extremely

important to photographers who wish to capture the beauty

of nature or a particular object. They are more vital in

computer vision research, where three-dimensional (3D)

images are providing data that can be used in a variety

of applications, including biometric identification for

homeland security, virtual reality, historical preservation,

and archaeology.

For example, faculty and students in the Computer

Vision Research Laboratory are applying 3D scanning,

modeling, and rapid prototyping to the fabrication of

missing bones in Peck’s Rex, one of

the highest-quality T.Rex skeletons ever

discovered. While an undergraduate in

the Department of Computer Science

and Engineering, Chris Boehnen wrote

a software program that automatically

converted digital photographs into files which described

the dimensional geometry of a shape for modeling

processes. As a graduate student, he is now applying

Nonprofit OrganizationU.S. Postage Paid

Notre Dame, IndianaPermit No. 10

Graduate student Chris Boehnenholds a lithopane — a translucentpiece of polymer, created throughrapid prototyping. When backlit, the lithopane looks like a three-dimensional photograph of the image on the lithopane.

rapid prototyping

techniques to

configure the

missing bones

of the T.Rex.

Boehnen; Patrick

J. Flynn, professor

of computer science and engineering; and J. Keith Rigby,

associate professor of civil engineering and geological

sciences, scanned the shape of the existing bones and

duplicated them at the correct scale and position to

complete the dinosaur. Replicas of their work are currently

on display in Notre Dame’s Eck Visitors’ Center.

Work in the Computer Vision Research Laboratory is

directed by Flynn and Kevin W. Bowyer, the Schubmehl-

Prein Chair in Computer Science and Engineering, and

supported by the National Science Foundation, Sandia

National Laboratories, and the Defense Advanced Research

Projects Agency.

For more information on 3D scanning, modeling, and

fabrication within the Department of Computer Science and

Engineering, visit http://www.cse.nd.edu/research/labs.php.